Iron in PDB 4f2n: Crystal Structure of Iron Superoxide Dismutase From Leishmania Major

Enzymatic activity of Crystal Structure of Iron Superoxide Dismutase From Leishmania Major

All present enzymatic activity of Crystal Structure of Iron Superoxide Dismutase From Leishmania Major:
1.15.1.1;

Protein crystallography data

The structure of Crystal Structure of Iron Superoxide Dismutase From Leishmania Major, PDB code: 4f2n was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.77 / 1.85
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 47.030, 102.740, 168.240, 91.66, 96.36, 95.01
R / Rfree (%) 17.3 / 20.3

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Iron Superoxide Dismutase From Leishmania Major (pdb code 4f2n). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Crystal Structure of Iron Superoxide Dismutase From Leishmania Major, PDB code: 4f2n:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 4f2n

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Iron binding site 1 out of 12 in the Crystal Structure of Iron Superoxide Dismutase From Leishmania Major


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Iron Superoxide Dismutase From Leishmania Major within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe300

b:17.3
occ:1.00
OD2 A:ASP191 1.9 16.6 1.0
NE2 A:HIS108 2.1 18.5 1.0
NE2 A:HIS58 2.2 15.9 1.0
NE2 A:HIS195 2.2 17.5 1.0
O A:HOH401 2.2 14.9 1.0
CG A:ASP191 3.0 16.4 1.0
CD2 A:HIS108 3.0 18.1 1.0
CE1 A:HIS108 3.1 17.9 1.0
CD2 A:HIS195 3.1 17.2 1.0
CE1 A:HIS58 3.1 15.9 1.0
CD2 A:HIS58 3.2 16.2 1.0
CE1 A:HIS195 3.2 17.3 1.0
OD1 A:ASP191 3.4 15.9 1.0
ND1 A:HIS108 4.1 17.6 1.0
CG A:HIS108 4.2 17.7 1.0
ND1 A:HIS58 4.3 16.2 1.0
CG A:HIS195 4.3 17.2 1.0
CZ2 A:TRP156 4.3 15.6 1.0
CG A:HIS58 4.3 16.6 1.0
CH2 A:TRP156 4.3 15.6 1.0
ND1 A:HIS195 4.3 17.1 1.0
CB A:ASP191 4.3 16.1 1.0
CB A:TRP193 4.5 15.7 1.0
CG A:TRP193 4.7 15.7 1.0
CB A:ALA196 4.8 16.3 1.0

Iron binding site 2 out of 12 in 4f2n

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Iron binding site 2 out of 12 in the Crystal Structure of Iron Superoxide Dismutase From Leishmania Major


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Iron Superoxide Dismutase From Leishmania Major within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe300

b:16.8
occ:1.00
OD2 B:ASP191 1.9 16.4 1.0
NE2 B:HIS108 2.1 16.3 1.0
NE2 B:HIS195 2.1 15.6 1.0
NE2 B:HIS58 2.2 16.0 1.0
O B:HOH483 2.3 12.3 1.0
CD2 B:HIS108 3.0 16.3 1.0
CE1 B:HIS108 3.0 16.2 1.0
CD2 B:HIS195 3.1 16.2 1.0
CG B:ASP191 3.1 16.1 1.0
CE1 B:HIS195 3.1 15.8 1.0
CE1 B:HIS58 3.1 17.2 1.0
CD2 B:HIS58 3.1 17.1 1.0
OD1 B:ASP191 3.5 15.7 1.0
ND1 B:HIS108 4.1 16.3 1.0
CG B:HIS108 4.2 16.5 1.0
ND1 B:HIS195 4.2 15.9 1.0
CG B:HIS195 4.2 16.2 1.0
CH2 B:TRP156 4.2 16.8 1.0
CZ2 B:TRP156 4.3 16.9 1.0
ND1 B:HIS58 4.3 17.2 1.0
CB B:ASP191 4.3 16.2 1.0
CG B:HIS58 4.3 17.6 1.0
CB B:TRP193 4.5 15.2 1.0
CG B:TRP193 4.8 15.0 1.0
CB B:ALA196 4.8 16.9 1.0

Iron binding site 3 out of 12 in 4f2n

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Iron binding site 3 out of 12 in the Crystal Structure of Iron Superoxide Dismutase From Leishmania Major


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Iron Superoxide Dismutase From Leishmania Major within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe300

b:21.2
occ:1.00
OD2 C:ASP191 1.9 20.7 1.0
NE2 C:HIS108 2.1 21.3 1.0
NE2 C:HIS195 2.2 18.8 1.0
O C:HOH402 2.2 18.5 1.0
NE2 C:HIS58 2.2 20.2 1.0
CG C:ASP191 3.0 20.2 1.0
CD2 C:HIS108 3.1 21.1 1.0
CE1 C:HIS108 3.1 21.2 1.0
CD2 C:HIS195 3.1 19.4 1.0
CE1 C:HIS58 3.2 20.3 1.0
CD2 C:HIS58 3.2 21.0 1.0
CE1 C:HIS195 3.2 18.9 1.0
OD1 C:ASP191 3.4 19.5 1.0
ND1 C:HIS108 4.2 21.5 1.0
CG C:HIS108 4.2 21.6 1.0
CH2 C:TRP156 4.2 19.3 1.0
CZ2 C:TRP156 4.3 20.0 1.0
CG C:HIS195 4.3 19.3 1.0
ND1 C:HIS195 4.3 19.0 1.0
CB C:ASP191 4.3 19.8 1.0
ND1 C:HIS58 4.3 21.4 1.0
CG C:HIS58 4.4 21.6 1.0
CB C:TRP193 4.5 18.9 1.0
CG C:TRP193 4.7 19.2 1.0
CB C:ALA196 4.8 19.8 1.0
CD1 C:TRP193 5.0 18.8 1.0

Iron binding site 4 out of 12 in 4f2n

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Iron binding site 4 out of 12 in the Crystal Structure of Iron Superoxide Dismutase From Leishmania Major


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Iron Superoxide Dismutase From Leishmania Major within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe300

b:21.1
occ:1.00
OD2 D:ASP191 1.9 19.1 1.0
NE2 D:HIS108 2.1 19.1 1.0
NE2 D:HIS58 2.1 20.0 1.0
NE2 D:HIS195 2.2 19.4 1.0
O D:HOH401 2.3 16.5 1.0
CD2 D:HIS195 3.0 20.0 1.0
CD2 D:HIS108 3.0 19.2 1.0
CG D:ASP191 3.0 19.0 1.0
CD2 D:HIS58 3.1 21.3 1.0
CE1 D:HIS58 3.1 20.4 1.0
CE1 D:HIS108 3.2 19.2 1.0
CE1 D:HIS195 3.3 19.9 1.0
OD1 D:ASP191 3.5 18.6 1.0
CG D:HIS108 4.2 19.8 1.0
ND1 D:HIS108 4.2 19.1 1.0
CG D:HIS195 4.2 19.8 1.0
ND1 D:HIS58 4.2 21.4 1.0
CG D:HIS58 4.3 21.5 1.0
CZ2 D:TRP156 4.3 19.5 1.0
CB D:ASP191 4.3 18.9 1.0
ND1 D:HIS195 4.3 19.9 1.0
CH2 D:TRP156 4.3 19.9 1.0
CB D:TRP193 4.5 18.1 1.0
CG D:TRP193 4.7 18.1 1.0
CB D:ALA196 4.9 20.3 1.0
NE2 D:GLN104 4.9 20.0 1.0

Iron binding site 5 out of 12 in 4f2n

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Iron binding site 5 out of 12 in the Crystal Structure of Iron Superoxide Dismutase From Leishmania Major


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Iron Superoxide Dismutase From Leishmania Major within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe300

b:16.9
occ:1.00
OD2 E:ASP191 1.9 16.1 1.0
NE2 E:HIS108 2.1 16.8 1.0
NE2 E:HIS58 2.2 14.8 1.0
O E:HOH401 2.2 15.7 1.0
NE2 E:HIS195 2.2 15.8 1.0
CE1 E:HIS108 3.0 16.8 1.0
CG E:ASP191 3.1 15.6 1.0
CD2 E:HIS108 3.1 16.9 1.0
CD2 E:HIS195 3.1 16.2 1.0
CE1 E:HIS58 3.1 14.8 1.0
CD2 E:HIS58 3.1 15.4 1.0
CE1 E:HIS195 3.3 15.9 1.0
OD1 E:ASP191 3.5 16.4 1.0
ND1 E:HIS108 4.1 16.7 1.0
CG E:HIS108 4.2 16.8 1.0
ND1 E:HIS58 4.3 15.4 1.0
CZ2 E:TRP156 4.3 15.2 1.0
CG E:HIS58 4.3 15.7 1.0
CG E:HIS195 4.3 16.4 1.0
CB E:ASP191 4.3 15.0 1.0
CH2 E:TRP156 4.3 15.0 1.0
ND1 E:HIS195 4.4 16.4 1.0
CB E:TRP193 4.5 14.3 1.0
CG E:TRP193 4.7 14.7 1.0
CB E:ALA196 4.8 14.9 1.0
NE2 E:GLN104 5.0 17.6 1.0

Iron binding site 6 out of 12 in 4f2n

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Iron binding site 6 out of 12 in the Crystal Structure of Iron Superoxide Dismutase From Leishmania Major


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Iron Superoxide Dismutase From Leishmania Major within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe300

b:19.8
occ:1.00
OD2 F:ASP191 1.9 20.9 1.0
NE2 F:HIS108 2.0 17.9 1.0
NE2 F:HIS195 2.2 19.9 1.0
NE2 F:HIS58 2.2 18.9 1.0
O F:HOH435 2.3 17.0 1.0
CD2 F:HIS108 3.0 18.2 1.0
CG F:ASP191 3.0 21.1 1.0
CE1 F:HIS108 3.1 17.8 1.0
CD2 F:HIS195 3.1 19.8 1.0
CD2 F:HIS58 3.1 19.4 1.0
CE1 F:HIS58 3.1 19.3 1.0
CE1 F:HIS195 3.2 19.1 1.0
OD1 F:ASP191 3.5 20.4 1.0
CG F:HIS108 4.1 18.3 1.0
ND1 F:HIS108 4.2 17.9 1.0
CH2 F:TRP156 4.2 19.5 1.0
ND1 F:HIS58 4.3 19.8 1.0
CZ2 F:TRP156 4.3 19.7 1.0
ND1 F:HIS195 4.3 19.2 1.0
CG F:HIS58 4.3 20.0 1.0
CG F:HIS195 4.3 19.6 1.0
CB F:ASP191 4.3 21.0 1.0
CB F:TRP193 4.5 17.9 1.0
CG F:TRP193 4.7 18.1 1.0
CB F:ALA196 4.8 20.4 1.0
NE2 F:GLN104 5.0 18.5 1.0

Iron binding site 7 out of 12 in 4f2n

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Iron binding site 7 out of 12 in the Crystal Structure of Iron Superoxide Dismutase From Leishmania Major


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Iron Superoxide Dismutase From Leishmania Major within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe300

b:16.8
occ:1.00
OD2 G:ASP191 1.9 15.9 1.0
NE2 G:HIS108 2.1 16.2 1.0
NE2 G:HIS58 2.2 17.9 1.0
O G:HOH459 2.2 14.5 1.0
NE2 G:HIS195 2.2 17.2 1.0
CG G:ASP191 3.0 17.0 1.0
CE1 G:HIS108 3.1 16.7 1.0
CD2 G:HIS108 3.1 16.2 1.0
CE1 G:HIS58 3.1 18.4 1.0
CD2 G:HIS195 3.1 17.4 1.0
CD2 G:HIS58 3.2 18.6 1.0
CE1 G:HIS195 3.2 17.2 1.0
OD1 G:ASP191 3.5 16.8 1.0
ND1 G:HIS108 4.2 16.7 1.0
CG G:HIS108 4.2 16.9 1.0
CH2 G:TRP156 4.3 17.7 1.0
ND1 G:HIS58 4.3 18.6 1.0
CB G:ASP191 4.3 16.9 1.0
CZ2 G:TRP156 4.3 17.5 1.0
ND1 G:HIS195 4.3 17.7 1.0
CG G:HIS58 4.3 18.9 1.0
CG G:HIS195 4.3 17.3 1.0
CB G:TRP193 4.5 15.4 1.0
CG G:TRP193 4.7 15.5 1.0
CB G:ALA196 4.8 17.0 1.0
NE2 G:GLN104 4.9 17.9 1.0
CD1 G:TRP193 5.0 15.5 1.0

Iron binding site 8 out of 12 in 4f2n

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Iron binding site 8 out of 12 in the Crystal Structure of Iron Superoxide Dismutase From Leishmania Major


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Iron Superoxide Dismutase From Leishmania Major within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe300

b:19.6
occ:1.00
OD2 H:ASP191 2.0 19.6 1.0
NE2 H:HIS195 2.1 18.9 1.0
NE2 H:HIS108 2.1 18.4 1.0
NE2 H:HIS58 2.1 16.6 1.0
O H:HOH401 2.3 16.6 1.0
CD2 H:HIS108 3.0 18.2 1.0
CD2 H:HIS195 3.1 18.9 1.0
CG H:ASP191 3.1 19.2 1.0
CE1 H:HIS58 3.1 17.8 1.0
CE1 H:HIS108 3.1 17.8 1.0
CE1 H:HIS195 3.1 18.7 1.0
CD2 H:HIS58 3.1 17.8 1.0
OD1 H:ASP191 3.5 18.7 1.0
ND1 H:HIS108 4.2 17.7 1.0
CG H:HIS108 4.2 17.7 1.0
ND1 H:HIS195 4.2 18.8 1.0
ND1 H:HIS58 4.2 18.0 1.0
CG H:HIS195 4.2 18.7 1.0
CG H:HIS58 4.3 18.2 1.0
CH2 H:TRP156 4.3 17.9 1.0
CZ2 H:TRP156 4.3 18.2 1.0
CB H:ASP191 4.3 18.8 1.0
CB H:TRP193 4.5 16.5 1.0
CG H:TRP193 4.7 17.0 1.0
CB H:ALA196 4.8 19.8 1.0

Iron binding site 9 out of 12 in 4f2n

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Iron binding site 9 out of 12 in the Crystal Structure of Iron Superoxide Dismutase From Leishmania Major


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Iron Superoxide Dismutase From Leishmania Major within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe300

b:20.4
occ:1.00
OD2 I:ASP191 2.0 22.1 1.0
NE2 I:HIS108 2.0 20.3 1.0
NE2 I:HIS58 2.1 22.4 1.0
O I:HOH401 2.1 18.2 1.0
NE2 I:HIS195 2.1 19.7 1.0
CD2 I:HIS108 3.0 20.6 1.0
CD2 I:HIS195 3.0 20.3 1.0
CE1 I:HIS58 3.0 22.3 1.0
CE1 I:HIS108 3.1 20.1 1.0
CG I:ASP191 3.1 20.4 1.0
CD2 I:HIS58 3.1 22.9 1.0
CE1 I:HIS195 3.2 19.6 1.0
OD1 I:ASP191 3.5 20.7 1.0
ND1 I:HIS108 4.1 20.2 1.0
CG I:HIS108 4.1 20.7 1.0
ND1 I:HIS58 4.2 21.8 1.0
CG I:HIS195 4.2 20.2 1.0
CG I:HIS58 4.3 22.4 1.0
ND1 I:HIS195 4.3 19.7 1.0
CZ2 I:TRP156 4.3 20.4 1.0
CH2 I:TRP156 4.3 20.8 1.0
CB I:ASP191 4.4 19.8 1.0
CB I:TRP193 4.5 18.8 1.0
CG I:TRP193 4.8 18.8 1.0
CB I:ALA196 4.8 19.9 1.0

Iron binding site 10 out of 12 in 4f2n

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Iron binding site 10 out of 12 in the Crystal Structure of Iron Superoxide Dismutase From Leishmania Major


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of Iron Superoxide Dismutase From Leishmania Major within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe300

b:19.2
occ:1.00
OD2 J:ASP191 1.9 17.4 1.0
NE2 J:HIS108 2.1 18.0 1.0
NE2 J:HIS58 2.2 18.2 1.0
NE2 J:HIS195 2.2 17.8 1.0
O J:HOH404 2.3 19.3 1.0
CE1 J:HIS108 3.0 17.7 1.0
CD2 J:HIS195 3.0 18.2 1.0
CG J:ASP191 3.1 17.3 1.0
CD2 J:HIS108 3.1 17.7 1.0
CE1 J:HIS58 3.1 18.8 1.0
CD2 J:HIS58 3.2 19.3 1.0
CE1 J:HIS195 3.2 17.7 1.0
OD1 J:ASP191 3.5 17.1 1.0
ND1 J:HIS108 4.2 17.6 1.0
CG J:HIS108 4.2 17.8 1.0
CG J:HIS195 4.3 18.3 1.0
ND1 J:HIS58 4.3 19.4 1.0
CZ2 J:TRP156 4.3 17.8 1.0
CH2 J:TRP156 4.3 18.2 1.0
CG J:HIS58 4.3 19.9 1.0
CB J:ASP191 4.3 17.4 1.0
ND1 J:HIS195 4.3 17.7 1.0
CB J:TRP193 4.4 16.4 1.0
CG J:TRP193 4.7 16.2 1.0
CB J:ALA196 4.8 18.6 1.0
NE2 J:GLN104 4.9 19.0 1.0
CD1 J:TRP193 5.0 16.1 1.0

Reference:

I.Q.Phan, D.R.Davies, N.S.Moretti, D.Shanmugam, I.Cestari, A.Anupama, J.W.Fairman, T.E.Edwards, K.Stuart, S.Schenkman, P.J.Myler. Iron Superoxide Dismutases in Eukaryotic Pathogens: New Insights From Apicomplexa and Trypanosoma Structures. Acta Crystallogr F Struct V. 71 615 2015BIOL Commun.
PubMed: 25961325
DOI: 10.1107/S2053230X15004185
Page generated: Sun Dec 13 15:33:33 2020

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